All Batches Excluding Those Recently Identified as Missing

[1] “01-0993 D0 AND 07-1147 DAY0_normalized–time_cut.fcs” [1] 3 1 2

01-0993 D0 AND 07-1147 DAY0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] "01_0673 d0 09_0462 d0 _1_1–time_cut.fcs" [1] 6 4 5

01_0673 d0 09_0462 d0 _1_1–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “01_0782 day0 and day180 06sep2017_normalized–time_cut.fcs” [1] 9 7 8

01_0782 day0 and day180 06sep2017_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “02-0185 DO AND 09-0296 D0 29SEP2017_normalized–time_cut.fcs” [1] 12 10 11

02-0185 DO AND 09-0296 D0 29SEP2017_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “03-0697 D0 and 03-0545 D0_normalized–time_cut.fcs” [1] 15 13 14

03-0697 D0 and 03-0545 D0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “03_0442 D0 and 09_0248 D0_normalized–time_cut.fcs” [1] 18 16 17

03_0442 D0 and 09_0248 D0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “03_0448 D0 and 09_0581 D0_normalized–time_cut.fcs” [1] 21 19 20

03_0448 D0 and 09_0581 D0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04-0718 D0 AND 04-0886 D0_normalized–time_cut.fcs” [1] 24 22 23

04-0718 D0 AND 04-0886 D0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04-0718 D180 AND 04-0886 D180_normalized–time_cut.fcs” [1] 27 25 26

04-0718 D180 AND 04-0886 D180_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04-0910 D360 AND 07-1132 D360_normalized–time_cut.fcs” [1] 30 28 29

04-0910 D360 AND 07-1132 D360_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04-1056 D360 PLUS 04-0979 D360_normalized–time_cut.fcs” [1] 33 31 32

04-1056 D360 PLUS 04-0979 D360_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_0152 D0 AND 04_0152 D180_normalized–time_cut.fcs” [1] 36 34 35

04_0152 D0 AND 04_0152 D180_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_0152 d360 and d540_3_1–time_cut.fcs” [1] 39 37 38

04_0152 d360 and d540_3_1–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_0238 d0and d180-2_normalized–time_cut.fcs” [1] 42 40 41

04_0238 d0and d180-2_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_0511 D0 AND 04_1119 D0_normalized–time_cut.fcs” [1] 45 43 44

04_0511 D0 AND 04_1119 D0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_0695 D360 and 04_0695 D540_normalized_–time_cut.fcs” [1] 48 46 47

04_0695 D360 and 04_0695 D540_normalized_–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_0695 do and d180_4_1–time_cut.fcs” [1] 51 49 50

04_0695 do and d180_4_1–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_0718 d360 and 04_0886 d360_normalized–time_cut.fcs” [1] 54 52 53

04_0718 d360 and 04_0886 d360_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_0741_d0 and d180_normalized–time_cut.fcs” [1] 57 55 56

04_0741_d0 and d180_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_0779 D0 AND 07_0369 D0_normalized–time_cut.fcs” [1] 60 58 59

04_0779 D0 AND 07_0369 D0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_0811D180 AND 07_1153 D180_normalized–time_cut.fcs” [1] 63 61 62

04_0811D180 AND 07_1153 D180_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_0843 D0 AND 04_0843 D180_normalized–time_cut.fcs” [1] 66 64 65

04_0843 D0 AND 04_0843 D180_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_0843 d360 and 04_0843 d540_normalized–time_cut.fcs” [1] 69 67 68

04_0843 d360 and 04_0843 d540_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_0910 d0 and 07_1132 d0_normalized–time_cut.fcs” [1] 72 70 71

04_0910 d0 and 07_1132 d0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_0910 D540 AND 07_1132 D540_normalized–time_cut.fcs” [1] 75 73 74

04_0910 D540 AND 07_1132 D540_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_1020 D360 and 04_1020 D540_normalized–time_cut.fcs” [1] 78 76 77

04_1020 D360 and 04_1020 D540_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_1020D0 and 04_1020 D180_normalized_–time_cut.fcs” [1] 81 79 80

04_1020D0 and 04_1020 D180_normalized_–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_1056 d0 and 04_0979 d0_normalized–time_cut.fcs” [1] 84 82 83

04_1056 d0 and 04_0979 d0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_1056 d180 and 04_0979 d180_normalized–time_cut.fcs” [1] 87 85 86

04_1056 d180 and 04_0979 d180_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_1104 d0 and d180_2_1–time_cut.fcs” [1] 90 88 89

04_1104 d0 and d180_2_1–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_1241 D0 AND 07_0119 D0_normalized–time_cut.fcs” [1] 93 91 92

04_1241 D0 AND 07_0119 D0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “04_1241 d180 and 07_0119 d180_normalized_–time_cut.fcs” [1] 96 94 95

04_1241 d180 and 07_0119 d180_normalized_–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “040238 d0and d180-2_normalized–time_cut.fcs” [1] 99 97 98

040238 d0and d180-2_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07-0135 DO AND 09-0406 DO. FCS_normalized–time_cut.fcs” [1] 102 100 101

07-0135 DO AND 09-0406 DO. FCS_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07-0259 D360 and 04-1067 D360_normalized–time_cut.fcs” [1] 105 103 104

07-0259 D360 and 04-1067 D360_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07-0262 D360 AND 540 27NOV2017_normalized–time_cut.fcs” [1] 108 106 107

07-0262 D360 AND 540 27NOV2017_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07-0262 DO AND D180 24NOV2017_normalized–time_cut.fcs” [1] 111 109 110

07-0262 DO AND D180 24NOV2017_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07-0692 D360 AND 04-1058 D360_normalized_–time_cut.fcs” [1] 114 112 113

07-0692 D360 AND 04-1058 D360_normalized_–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0060 D360 AND 04_0699 D360_normalized–time_cut.fcs” [1] 117 115 116

07_0060 D360 AND 04_0699 D360_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0150 D0 AND D180_2_1–time_cut.fcs” [1] 120 118 119

07_0150 D0 AND D180_2_1–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0177 D0 AND 07_0177 D180_normalized–time_cut.fcs” [1] 123 121 122

07_0177 D0 AND 07_0177 D180_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0208 D0 and D540_normalized–time_cut.fcs” [1] 126 124 125

07_0208 D0 and D540_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0214 DE360 and D540_normalized_–time_cut.fcs” [1] 129 127 128

07_0214 DE360 and D540_normalized_–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0236 D0 AND D180_3_1–time_cut.fcs” [1] 132 130 131

07_0236 D0 AND D180_3_1–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0259 d0 and 04_1067 d0_normalized–time_cut.fcs” [1] 135 133 134

07_0259 d0 and 04_1067 d0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0386 D0 and D540_normalized–time_cut.fcs” [1] 138 136 137

07_0386 D0 and D540_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0390 D0 and D540_normalized–time_cut.fcs” [1] 141 139 140

07_0390 D0 and D540_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0424 d0 and d540_normalized_–time_cut.fcs” [1] 144 142 143

07_0424 d0 and d540_normalized_–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0425D0 and D180_normalized–time_cut.fcs” [1] 147 145 146

07_0425D0 and D180_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0561 D0 AND D180_normalized–time_cut.fcs” [1] 150 148 149

07_0561 D0 AND D180_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0630 D0 AND 07_0630 D180_normalized_–time_cut.fcs” [1] 153 151 152

07_0630 D0 AND 07_0630 D180_normalized_–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0630 d360 and 07_0630 d540_normalized–time_cut.fcs” [1] 156 154 155

07_0630 d360 and 07_0630 d540_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] "07_0663 d360 and 07_0663 d540 _2_normalized–time_cut.fcs" [1] 159 157 158

07_0663 d360 and 07_0663 d540 _2_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0692 D0 AND 04_1058 D0_normalized–time_cut.fcs” [1] 162 160 161

07_0692 D0 AND 04_1058 D0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0692 d180 and 04_1058 d180_normalized–time_cut.fcs” [1] 165 163 164

07_0692 d180 and 04_1058 d180_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_1003 day360 and day540_normalized–time_cut.fcs” [1] 168 166 167

07_1003 day360 and day540_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_1115_1_1–time_cut.fcs” [1] 171 169 170

07_1115_1_1–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_1153 D540 AND 07_0811 D540_4_1–time_cut.fcs” [1] 174 172 173

07_1153 D540 AND 07_0811 D540_4_1–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_1158 d360 and 07_1158 d540_normalized_–time_cut.fcs” [1] 177 175 176

07_1158 d360 and 07_1158 d540_normalized_–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “09_0314 D0 AND 01_0978 D0_normalized–time_cut.fcs” [1] 180 178 179

09_0314 D0 AND 01_0978 D0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “09_0453 d0 and 09_0745 D0_normalized–time_cut.fcs” [1] 183 181 182

09_0453 d0 and 09_0745 D0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “09_0467 d0 and 09_0278 d0_normalized_–time_cut.fcs” [1] 186 184 185

09_0467 d0 and 09_0278 d0_normalized_–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “09_0507 d0 09_0587 d0_normalized–time_cut.fcs” [1] 189 187 188

09_0507 d0 09_0587 d0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “09_0569 D0 and 09_0529 D0_normalized–time_cut.fcs” [1] 192 190 191

09_0569 D0 and 09_0529 D0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “09_0789 D0 AND 09_0712 D0_normalized–time_cut.fcs” [1] 195 193 194

09_0789 D0 AND 09_0712 D0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “29NOV2017 07-0080D360 AND 07-0080 D540_normalized–time_cut.fcs” [1] 198 196 197

29NOV2017 07-0080D360 AND 07-0080 D540_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “30NOV2017 07-0080 DAY0 AND 07-0080 DAY180_normalized–time_cut.fcs” [1] 201 199 200

30NOV2017 07-0080 DAY0 AND 07-0080 DAY180_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “frozen 07_0060 d180 and 04_0699 d180_6_1–time_cut.fcs” [1] 204 202 203

frozen 07_0060 d180 and 04_0699 d180_6_1–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “FROZEN 20FEB TO 09MAR_ 07_1153 D360 AND 07_0811 D360_normalized–time_cut.fcs” [1] 207 205 206

FROZEN 20FEB TO 09MAR_ 07_1153 D360 AND 07_0811 D360_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “FROZEN_04_1241 d360 and 07_0119 d360_normalized_–time_cut.fcs” [1] 210 208 209

FROZEN_04_1241 d360 and 07_0119 d360_normalized_–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “FROZEN_07_0060 D0 AND 04_0699D0_normalized–time_cut.fcs” [1] 213 211 212

FROZEN_07_0060 D0 AND 04_0699D0_normalized–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “miguel-concat-replace-04_0333_D0_AND_D180_1_TOGETHER_1–time_cut.fcs” [1] 216 214 215

miguel-concat-replace-04_0333_D0_AND_D180_1_TOGETHER_1–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “miguel-from_r-06_0127 and 06_0127b_5_1–time_cut.fcs” [1] 219 217 218

miguel-from_r-06_0127 and 06_0127b_5_1–time_cut.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

Previously missing CyTOF files

[1] “07_0177 d360 and 07_0177 d540_cells_found_normalized_debeaded.fcs-.fcs” [1] 3 1 2

07_0177 d360 and 07_0177 d540_cells_found_normalized_debeaded.fcs-.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition

[1] “07_0663 D0 AND 07_0663 D180_cells_found_normalized_debeaded.fcs-.fcs” [1] 6 4 5

07_0663 D0 AND 07_0663 D180_cells_found_normalized_debeaded.fcs-.fcs

IFNg vs Beads for live singlets

IFNg vs beads for live singlets by stim condition

IFNg vs TNF for CD4 T cells by stim condition